Complete genome analysis of Enterococcus hirae S2 from the gut of Large-Tailed Han sheep reveals genomic potential for bacteriocin production and multidrug resistance risk

The global spread of antimicrobial resistance (AMR) urgently calls for novel antibacterial lead compounds. The animal intestinal tract serves not only as a reservoir of resistance genes but also as an underexplored source of antimicrobial metabolites. Enterococcus hirae ( E. hirae ), a commensal gut bacterium, has not yet been systematically characterized with respect to the genomic potential for beneficial metabolite production and its associated resistance risk. Hybrid Illumina and PacBio sequencing was employed to determine the complete genome of E. hirae strain S2, isolated from the ileal contents of a healthy Large-Tailed Han sheep. The genome comprises a circular chromosome (2.87 Mb) and two plasmids (pA and pB). Five biosynthetic gene clusters (BGCs) were identified, including a complete type II lanthipeptide cluster ( lanM ) and two Agr quorum-sensing systems, indicating potential for novel bacteriocin production. Nine acquired resistance genes or mutations were detected, conferring genotypic resistance to elfamycins, daptomycin, aminoglycosides, and efflux-mediated multidrug resistance. Phenotypic assays confirmed resistance to cephalosporins, streptomycin, polymyxin B, and clindamycin. Mobile genetic elements (plasmids, genomic islands, and prophages) suggest horizontal gene transfer potential. The strain also harbors 16 virulence factors and 54 carbohydrate-active enzymes, with rapid acid producing capability (pH 6.32 at 6 h). E. hirae strain S2 harbors the genomic potential for novel antimicrobial metabolite (lanthipeptide/bacteriocin) biosynthesis while simultaneously carrying genetic determinants that may contribute to the dissemination of AMR. This study provides precise genetic evidence supporting the exploration of anti-drug-resistant metabolites derived from commensals within specific ecological niches, while also underscoring the necessity of concurrently assessing resistance and virulence risks during the development and application of such strains.